DNA Flow-Stretch Assays for Studies of Protein-DNA Interactions at the Single-Molecule Level

Protein-DNA interactions are the core of the cell’s molecular machinery. For a long time, conventional biochemical methods served as a powerful investigatory basis of protein-DNA interactions and target search mechanisms. Currently single-molecule (SM) techniques have emerged as a complementary tool for studying these interactions and have revealed plenty of previously obscured mechanistic details. In comparison to the traditional ones, SM methods allow direct monitoring of individual biomolecules. Therefore, SM methods reveal reactions that are otherwise hidden by the ensemble averaging observed in conventional bulk-type methods. SM biophysical techniques employing various nanobiotechnology methods for immobilization of studied molecules grant the possibility to monitor individual reaction trajectories of biomolecules. Next-generation in vitro SM biophysics approaches enabling high-throughput studies are characterized by much greater complexity than the ones developed previously. Currently, several high-throughput DNA flow-stretch assays have been published and have shown many benefits for mechanistic target search studies of various DNA-binding proteins, such as CRISPR-Cas, Argonaute, various ATP-fueled helicases and translocases, and others. This review focuses on SM techniques employing surface-immobilized and relatively long DNA molecules for studying protein-DNA interaction mechanisms.

Innovative Skin Product O/W Emulsions Containing Lignin, Multiwall Carbon Nanotubes and Graphene Oxide Nanoadditives with Enhanced Sun Protection Factor and UV Stability Properties

In the present study, oil-in-water (O/W) sunscreen emulsions were prepared containing different portions of lignin (LGN), multiwall carbon nanotubes (MWCNTs) and graphene oxide (GO) nanoadditives. The stability in terms of pH and viscosity of emulsions was thoroughly studied for up to 90 days, exhibiting high stability for all produced O/W emulsions. The antioxidant activity of emulsions was also analyzed, presenting excellent antioxidant properties for the emulsion that contains LGN due to its phenolic compounds. Moreover, the emulsions were evaluated for their ultraviolet (UV) radiation protection ability in terms of sun protection factor (SPF) and UV stability. SPF values varied between 6.48 and 21.24 while the emulsion containing 2% w/v MWCNTs showed the highest SPF index and all samples demonstrated great UV stability. This work hopefully aims to contributing to the research of more organic additives for cosmetic application with various purposes.

Fast Orbital-Free Full-Potential Calculations for Large Nano Objects: C, Al and Ti

In the context of a full-potential orbital-free approach for the modeling of multi-atomic systems we investigated the dependence of the cohesive energies and bulk elastic modules of the large nanosystems Cn (n is up to 4096 atoms), Aln (n is up to 23,328 atoms) and tin (n is up to 2160 atoms). It was shown that the cohesive energies and elastic modules tend towards bulk crystal values at n ≈ 3000 for Cn systems, at n ≈ 1500 for Tin and at n ≈ 20,000 for Aln. The execution time for one energy iteration for Ti23328 was only 23 min.

Synthesis, Characterization and Catalytic Activity of UiO-66-NH2 in the Esterification of Levulinic Acid

The massive use of petroleum and its possible exhaustion are driving the current research trend to study alternative raw materials from biomass for organic reactions. In this context, the present article presents a study of the catalytic esterification of levulinic acid, a platform molecule, with ethanol. Metal-organic framework (MOF) type compounds UiO-66-NH2 have been synthesized. Zirconium was incorporated, using zirconium chloride as a metal precursor, together with 2-aminoterephthalic acid as an organic binding agent. An alternative route of synthesis was proposed using more favorable conditions from an economic and environmental point of view, replacing dimethylformamide by 50 and 75% acetone as substitute solvent. The physicochemical properties of the materials were evaluated by X-ray diffraction (XRD), Infrared Spectrometry with Fourier Transform (FTIR), scanning electron microscopy (SEM), X-ray photoelectron spectroscopy (XPS), microwave plasma atomic emission spectroscopy (MP-AES) and N2 adsorption to understand their morphology, crystalline, chemical and pore structure. The progress of the reaction was followed by gas chromatography and mass spectroscopy. The catalytic activity result of MOF25% in autoclave reactor, showed 100% of selectivity to ethyl levulinate and a turnover number (TON) of 66.18 moles of product/moles of Zr. This good catalytic performance obtained by partial solvent replacement in the synthetic material provides a more economical and eco-friendly process for ethyl levulinate generation.

Low-Cost Nanostructured Thin Films as Covert Laser Readable Security Tags for Large-Scale Productions Tracking

We report here the feasibility study of anti-counterfeiting low-cost nanostructured flexible security tags for the tracking of large-scale fabrication products, such as pharmaceuticals or original equipment manufacturers. The fabrication process makes use of the mature nanotechnology called Template Synthesis to shape thin track-etched polymer film into covert laser readable tags, combining random self-organized structures with organized patterns. Techniques are developed to drastically limit the number of fabrication steps and keep fabrication costs low, while opening to numerous adjustment parameters. A dedicated, simple optical setup is presented, to capture speckle images of such tags lightened up by light emitting diodes or laser beams. Speckle images are analyzed in terms of encoding parameters, found here quite numerous to ensure a large coding range of large-scale production batches. We particularly highlight ultra-dark areas in speckle images, where nanowire structures completely inhibit speckle patterns. This unique, high-contrast optical feature addresses these low-cost nanostructured thin films to provide a very promising solution for large-scale security tags.

Platinum Deposited Nitrogen-Doped Vertically Aligned Carbon Nanofibers as Methanol Tolerant Catalyst for Oxygen Reduction Reaction with Improved Durability

Nitrogen doping in carbon materials can modify the employed carbon material’s electronic and structural properties, which helps in creating a stronger metal-support interaction. In this study, the role of nitrogen doping in improving the durability of Pt catalysts supported on a three-dimensional vertically aligned carbon nanofiber (VACNF) array towards oxygen reduction reaction (ORR) was explored. The nitrogen moieties present in the N-VACNF enhanced the metal-support interaction and contributed to a reduction in the Pt particle size from 3.1 nm to 2.3 nm. The Pt/N-VACNF catalyst showed better durability when compared to Pt/VACNF and Pt/C catalysts with similar Pt loading. DFT calculations validated the increase in the durability of the Pt NPs with an increase in pyridinic N and corroborated the molecular ORR pathway for Pt/N-VACNF. Moreover, the Pt/N-VACNF catalyst was found to have excellent tolerance towards methanol crossover.

Towards Cellular Ultrastructural Characterization in Organ-on-a-Chip by Transmission Electron Microscopy

Organ-on-a-chip technology is a 3D cell culture breakthrough of the last decade. This rapidly developing field of bioengineering intertwined with microfluidics provides new insights into disease development and preclinical drug screening. So far, optical and fluorescence microscopy are the most widely used methods to monitor and extract information from these models. Meanwhile transmission electron microscopy (TEM), despite its wide use for the characterization of nanomaterials and biological samples, remains unexplored in this area. In our work we propose a TEM sample preparation method, that allows to process a microfluidic chip without its prior deconstruction, into TEM-compatible specimens. We demonstrated preparation of tumor blood vessel-on-a-chip model and consecutive steps to preserve the endothelial cells lining microfluidic channel, for the chip’s further transformation into ultrathin sections. This approach allowed us to obtain cross-sections of the microchannel with cells cultured inside, and to observe cell adaptation to the channel geometry, as well as the characteristic for endothelial cells tight junctions. The proposed sample preparation method facilitates the electron microscopy ultrastructural characterization of biological samples cultured in organ-on-a-chip device.

Copper and Nickel Nanoparticles Prepared by Thermal Treatment of Their Respective Cations Confined in Nanopores through High-Pressure Synthesis

A new and simple method for preparing confined copper and nickel nanoparticles by thermal treatment of their respective cations inside Mobil Composition of Matter 41 (MCM–41) hydrophobic nanopores is presented here. Surface modified MCM–41 hydrophobic materials were impregnated by using high-pressure treatment with copper II (Cu II) or nickel II (Ni II) aqueous solutions. After pressure release and washing, the remaining metal cations, confined exclusively within the nanopores, were heated, forming metallic nanoparticles. Reduction of the cations by a redox reaction between the hydrophobic organic surface and the confined metal cations is proposed. Transmission electronic microscopy (TEM), selected area electron diffraction (SAED), nitrogen (N2) adsorption at −196 °C (77 K), Fourier transform infrared (FTIR) and thermogravimetric (TGA) analyses evidenced the identification of copper and nickel nanoparticles (NPs).

Importance of Doping Sequence in Multiple Heteroatom-Doped Reduced Graphene Oxide as Efficient Oxygen Reduction Reaction Electrocatalysts

Multiple heteroatom-doped graphene is of great interest for developing an efficient electrocatalyst for oxygen reduction reaction (ORR). To maximize the electrocatalytic performance of doped graphene, the competitive doping mechanism caused by the different atomic sizes of dopants should be developed. Herein, three different heteroatoms (e.g., N, P and B) are competitively introduced into reduced graphene oxide (RGO) using both single- and two-step processes. The total quantity of heteroatoms for ternary RGO synthesized using the two-step process is lower than that when using the single-step process. Higher ORR electrocatalytic activity for the two-step-synthesized RGO compared to the single-step-synthesized RGO can be explained by: (a) a high amount of P atoms; (b) the fact that B doping itself decreases the less electrocatalytic N moieties such as pyrrole and pyridine and increases the high electrocatalytic moieties such as quaternary N; (c) a high amount of B atoms itself within the RGO act as an electrocatalytic active center for O2 adsorption; and (d) a small amount of substitutional B might increase the electrical conductivity of RGO. Our findings provide new insights into the design of heteroatom-doped carbon materials with excellent electrocatalytic performance.

Design of ZnO-Drug Nanocarriers against the Main Protease of SARS-CoV-2 (COVID-19): An In Silico Assay

The treatment of coronavirus diseases (COVID-19) is a principal aim worldwide that is required restore public health in the population. To this end, we have been studied several kinds of de novo and repurposed drugs to investigate their ability to inhibit the replication of the virus which causes the current pandemic—the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, finding a vehicle that promotes the controlled dosage is vital for avoiding secondary effects. For this reason, the present work exposes a nanostructured carrier based on ZnO, which is coupled to three repurposed drugs (Chloroquine, Dipyridamole, and Lopinavir) to understand the chemical interaction of the formed composite. The designed composites are modeled and optimized using the DFT formalism. In obtaining exergonic adsorption energies, we found values between 0.582 to 2.084 eV, depending on the used drug. At the same time, the HOMO orbitals demonstrate the electronic overlap between the ZnO-Np and the Lopinavir, which is the molecule with the higher adsorption energy. Finally, we carried out a docking assay to investigate the interaction of free drugs and composites with the main protease of the SARS-CoV-2, finding that the coupling energy of the composites (at around to 0.03 eV) was higher, compared with the free drugs. As such, our results suggest a controlled dosage of the drug on the SARS-CoV-2 target.